The Price You Must Pay
by Steefwaterbutter
Summary: "Do you ever think about the lives you have stolen?" On a simple pitstop with Derpy to watch a sunset, the Doctor finds himself kidnapped by the Shadow Ponies, a species obsessed with justice. Their job: make him pay for the lives he has taken. T for injuries.
1. Part 1

Before the Shadow Ponies, before the torture, before the grief, it was just a simple sidestop. Not even a fully-fledged trip, just a walk around Reb'lar, a gorgeous planet "known for it's absolutely stunning sunsets, if I do say so myself, Miss Hooves." They had decided to explore some of the tunnels under ground when they were discovered by the Shadow Ponies.

Derpy had seen many strange species during her travels with the Doctor, but none chilled her bones quite like these. Even the Doctor pinned his ears and snapped his tail at the sight of them.

The Shadow Pony slippped across the wall towards them, gliding smoothly without even moving his body. Then he seemed to materialize in front of them, drawing himself up to his full hight. He was coal-black all over, except for his eyes which gleamed purple, reflecting off the light the Doctor was casting with his horn. When he spoke, his voice was hissing and echoey, snaking out his mouth to ring in Derpy's ears.

"Oh my. The Doctor... this is very flattering, meeting with such a celebrity. Allow me to introduce myself. I am Taldusk the Shadow Pony."

At first his tone was mocking, then it abruptly deepened to a growl. "I wonder... Do you ever think about the lives you have stolen?"

Derpy snuck a glance at the Doctor, and saw his lip curled, almost in a snarl. Hesitantly, Derpy took a step back. She had never seen the Doctor get this angry so quickly before.

"Get ready to run, Derpy," he whispered to her almost inaudiably. "Only, this time, run faster than you ever have before,"

Derpy kept her eyes trained on the Shadow Pony and nodded slightly, already feeling her adrenalin rise.

"Do you ever stop to question _just how many_ enemies you have made?" the Taldusk spat.

Almost as soon as the last word left his mouth, the wall of the cavern gleamed with purple... the purple eyes of the Shadow Ponies.

"The day of judgement has come at last, Doc-_tor_."

"Derpy, _run,_" the Doctor whispered through gritted teeth.

For a moment she stood, unable to move, staring all around her at the shimmering eyes.

"RUN!" the Doctor shouted, shoving her, and this time, she ran.

She had been traveling so long with the Doctor that the running was almost instinctive now. Run. Don't stop, don't look back. Just _run._

Over her time with the Doctor, Derpy had become fleet of foot, and it was several minutes before she slowed down enough to realize that she was alone.

"Doctor?" she called out tentatively, straining her ears, trying to make out the distant sound of drumming hooves. "_Doctor_?!"

Nothing.

_Oh no. They must have taken him!_

With that terrible thought in mind, Derpy turned and began to run once more.

* * *

At first it was nothing more than noise, the words going in one ear and out the other, but carrying no meaning. Then, slowly, the words were pieced together.

"Heard... you... so many... say the most dangerous thing about you is your voice, your words. Of course I took the precaution to make sure you won't be able to use it. Ah, the humble Equestrian duct tape. Spares me from having to listen to stupid whining, _and _keeps the world's most dangerous weapon contained. So useful."

The Doctor's eyes shot open, and he felt his whole body tense as he sucked in breath from his nose. He was in a room, a blank white room, with a tiled floor, strapped to a wooden table of sorts. But just _where, _exactly, _was he? _What had happened to him? Where was he? Who was talking?

Then he remembered. Jumped. He'd been careless, waited a split second too long, and the Shadow Ponies had surrounded him. Even with his magic and reflexes, he hadn't been able to act, couldn't even open his mouth to try and reason with them, before _something _had smacked the side of his skull and knocked him out. Lovely.

But Derpy, where was Derpy? Had they taken her too? Had she gotten away?

"We are not a barbaric species, but we do have a strong sense of justice," he heard the voice murmer from the shadows. It was Taldusk, the Shadow Pony who had confronted them in the cavern. "Those who disobey must be _punished._" He paused for a second, then continued in an almost bored tone, as if eager to get the explaining done, "There were some among us who said we should kill your companion, make you feel the pain of loss, but her crimes are not like yours. She does not deserve punishment."

The Doctor closed his eyes, slumping against the table. _They won't harm her. They'll let her go._

"But they did agree you should lose something." Taldusk paused, and when he spoke again, the two words were like a knife in the Doctor's gut.

"Your horn."

_"No! Oh please, _no_!"_ A muffled scream tried to wrench itself out of the Doctor's closed mouth, but it was in vain.

He squeezed his eyes shut and did not open them. He would not open his eyes and let his enemies see the terror that reverberated through his body with the banging of his hearts against his chest.

_Calm. _He tried to black his mind, to rid it of all thoughts other than _Derpy is all right. They won't hurt her. They won't hurt her. She's safe._

_Unless she interferes with their judgement._

The Doctor knew that that was the highest offence one could commit while dealing with the Shadow Ponies. Interrupt, make one move to free to accused, and they would kill you without a moment's hesitation.

"Shall we get this over with, Doctor?"

The voice was different than Taldusk's. It was flat and emotionless, yet still held the slightest hint of pity.

Oh, if he could speak,_ if only he could speak!_

But he could not. So he simply kept his eyes shut and waited for it to be over.

At first there was silence, broken only by the thudding of his hearts. Then someone started screaming.

For a moment there was _pain, _pain that turned his vision red, pain that was worse than fire, pain that burned through him like acid.

Then there was blackness, but even here the torturous agony followed him. Something wet was sliding down his face, nearly dripping into his eye. He shuddered again and again, but he could not rid himself of the feeling that _something was missing._

"D-Doctor?"

It was Derpy, her worried face sliding and out of focus as she hovered above him. Then the blackness consumed her, her voice fading to an echo.

"D-don't worry, Doctor. I'm c-coming... hold on. Just hold... on..."

_Bright Eyes... dear, loyal Bright Eyes... no... they'll kill you... Run, _he though wearily, lifting his gaze to meet hers.

Then came the voice of Taldusk, breaking through the blackness.

"Run, Doctor."

His body slammed into stone and the breath was driven from his lungs. For a second he lay there, trying to gather his wits, then opened his eyes.

He was in yet another room, a dark cavern. The walls around him were composed of jagged stones. Soft, natural light poured in from a hole in the ceiling, creating a circle of light upon the cold floor.

"The legends spoke of how you ran: always, _always_ running," he heard Taldusk say from across the room. He narrowed his purple eyes and lifted his lips in a grin. "I want to see that. I want to see you _run."_

The Doctor had no breath to respond. He could feel a black eye forming, his eye nearly swollen shut, and his hair was matted, sticking to his forehead. The rest his body ached and stung, sweat dripping into some of the cuts.

He tried to stand up, but his legs slid out from under him, and his expression controted as a white-hot pang shot through one of his front legs. He looked down and gasped. The lower half was bent slightly, the area swollen and turning purplish-blue. Fractured, possibly broken.

Taldusk stepped closer to him and the Doctor pinned his ears, his teeth gritted, and his eyes shinning with unshed tears from every throbbing ache.

"Oh how I love to see the guilty receive justice for what they have done," the Shadow Pony murmered, looking over the Doctor with satisfaction.

_How can you take pleasure in other's pain? How? _

He watched numbly as Taldusk glided towards the door, a rectangular hole of sorts in the wall. A part of the Doctor wanted to get up and try and run out the door, but he knew Taldusk would be able to shove him over easily. So instead, he spoke.

"I gave them.. a chance," the Doctor said, taking a shuddering breath. They had taken the tape off his mouth, and he needed to take advantage of that. He had to try...

Taldusk stood stiffly, turned away from the Doctor, but his ears were swiveled back, listening.

"They... had a _choice,_" the Doctor continued, quiet but determined. "They could have..." He coughed, his throat feeling raw. "Have _chosen to go_, and… I would… have let them, I would have _helped them."_

"Not always, Doctor. Not everyone."

At last Taldusk turned, but his gaze was hard, unforgiving. "You're not as perfect as you make yourself out to be."

With that, Taldusk walked stiffly out the door, placing his hoof on something on the other side of the wall. He looked down at it, then back at the Doctor.

"Oh, and one more thing, Doctor_..." _he called mockingly. "Stay out of the shadows."

* * *

_Which way, _which way? Derpy thought frantically, casting her good eye back and forth between the two tunnels. One was blocked by a metal lattice grille... a portcullis, the other was open. After a second, she face-hoofed.

"Oh course, the one with the portcullis!" she exclaimed jumping up to hover in the air. She raised her hoof to her mouth and chewed on it nervously. "But how do I get past it?"

She studied the gaps inbetween the bars for a moment, then said, "Maybe I can squeeze through..."

First Derpy thrust her head and forelegs through the gap, then by pushing her hooves against the flat metal beams and sucking in her breath, she pulled her torso through. Then she let out a squeak. She was stuck. Derpy tried to push harder, but the beams scraped painfully against her coat, causing her to cry out.

Ahead of her a voice shouted shouted in alarm, and the sound of hoofbeats came pounding towards her. For a moment she wriggled and pushed frantically, then popped out, landing in a heap on the floor with an "Oof!" She was up in an instant, soaring through the air, and over the head of a Shadow Pony, a different one than they had met before.

He skidded to a stop and lept up into the air behind her. Derpy desperately whipped her tail up. She must have caugh him in the eye, because a second later she heard his cry of pain, and the thud as he hit the floor.

Still flapping her wings as fast as she could, Derpy looked back and saw the rapidly shrinking image of the shadow guard sitting on the ground, one hoof held up to his eye.

"Um, oops?" Derpy squeaked apologetically. She _had _meant to hit him with her tail, but she still felt bad for doing it.

She directed her gaze forward again and nearly screamed.

"Woah, woah, WOAH! EEK!"

Directly in front of her was a room filled with tables, chairs, bags, everything. And she was headed straight towards them.

Derpy squeezed her eyes shut and slammed her wings straight open in an effort to slow down.

The first thing she hit was a chair. Then the chair slammed a wobbly table which which tipped over with a loud bang. The crash startled Derpy so much she stumbled back and tipped over some bags full of metal instruments, the contents spilling out across the floor.

Derpy sighed, cringing slightly. "Oh dear."

Her ears pricked again as the sound of pounding hooves reached her ears. The Shadow Ponies.

Derpy quickly rose and shut the heavy metal door. Then, just for good measure she pushed a table against it. She grabbed chairs and heavy tools, all piling them in front of the door.

_There. That should take them a while, _she thought, looking over her work.

"Now to find the Doctor..."

* * *

It hurt. It hurt to drag his broken body up the rocky slope, towards the light. He was shivering and sweating, he had lost all feeling in his front leg, and _his horn was gone._ A piece of his body, his flesh and bone, had been broken off and left behind. A part of himself was gone... perhaps forever. It _hurt_.

The shadows stretched up behind him, seeming to taunt him. Perhaps the Shadow Pony had been lying, after all, why would he risk staying in the room so long? Perhaps his eyes were playing tricks on him, and there was no Vashta Neirada. But he could not take that chance, and he _would not _just give up and die. He was the Doctor, and he would not stop fighting until every last bit his strength was spent.

So he climbed. Every step was torment, but he would not stop. Pain threatened to consume him like the Vashta Neirada would soon consume his flesh. But he would not give up. The Doctor climbed, he climbed on and on, with the shadows stretching their fingers behind him, toying with him.

He climbed until he could climb no more.

The light brown stallion, the hornless unicorn collapsed on the rock, sobbing for breath, shaking and shivering from the cold that brushed across his sweat-soaked body. Everything throbbed: his eye, his leg, what little was left of his horn. They called it justice... but where was their mercy?

"I... tried to... offer them mercy," he whispered, staring blankly into the endless darkness. "But they never took it."

* * *

**A/N: This is my first "dream movie" I've postd on here that I haven't dramatically changed. In fact, I barely had to chance the plot at all. **

**I got the main idea from 2 sources: the Doctor Whooves and Assistant audio drama "Frostbite", CannedCream's MLP analysis video "Broken Horns" and the image of Derpy's hoof spashing through a puddle in a cave as she ran.**

**"Frostbite" gave me the initial idea of "What if some people got angry with the Doctor about all the lives he's taken?"**

**"Broken Horns"... I wanted to add a "bit" more whump, and the video provided me with information on how to do it.**

**Yeah, I was lazy on coming up with a design and name for the species. I based the Shadow Ponies off the Ender Ponies from the music video parody "Don't Mine at Night". I did go a bit more in-depth about what exactly they do. Just ask, and I will give you my (_sort of_) lengthy explanation.**

**BUT ANYWAAAAYYYYY, if you want to read the original "script" version, head on over to my Devaintart page (my username is Startoucher) and you should be able to find it easily. **


	2. Part 2

**A/N: BRACE THYNESELF FOR ZE FLUFFY HURT/COMFORT at the end. :D**

* * *

He was lying in a lifeless heap when she saw him, the light shinning down from above, washing over his bruised and broken body.

Her Doctor.

Her friend, her protector, the stallion who had swept her off her hooves amd shown her the stars.

And he was dying.

"Oh no," she whispered. "Oh no."

She landed gently on the rock on which he was lying, and stepped hesitantly forward, trying to focus her eyes, which seemed to want to look away from the horrible scene.

"Doctor?"

A feeble cough came from the Doctor, and she was at his side in an instant, tears pooling in her eyes. He looked up at her and Derpy felt her heart clench. His eyes were glassy, unfocused.

"Doctor... y-your horn..."

The Doctor blinked, his eyes clearing slightly. "Yes, Derpy. They... took my horn. But Derpy, you see... I've always wondered what it would be like to be an... earth pony," the Doctor tried to say lightheartedly, but his voice sounded hoarse and strained, and he broke off coughing.

"Doctor..." Derpy began.

"Blimey... it _hurt, _though. And, ah, I think they may have fractured my leg."

"_Doctor_!"

"I mean, I can deal with the broken horn, at least for now, anyway, but did they _really _have to break my leg t-"

"Doctor, stop it! Just stop it!" Derpy choked, slamming her hoof down on the rock. "We need to get out of here!"

The Doctor looked at her and shook his head slightly, his eyes big and soft and sad. "I'm sorry, Derpy," he said quietly. "It's bad enough you've come in here. If you take me... and they catch you... they will do _even more horrible_ things to you." His expression hardened. "And I _can't_ let that happen. I can't have another life on my conscience. Not now. Not today."

"No." Derpy slipped forward and rested her chin on the Doctor's neck, letting out a sigh. "I'm _not _leaving you here to die. I can't. _I _wouldn't be able to live with your death on my conscience. Not now, and not today," she echoed.

She took a breath, then quickly slid herself under his stomach so when she stood, he was draped across her back.

"Doctor," she told him. "I don't think you're a unicorn _or _an earth pony. You're as light as a pegasus."

"Yes, I-I've been dieting," the Doctor remarked wryly.

Derpy crouched on the rock, then jumped, straining her wings to carry both herself and the Doctor. For few moments she pumped vigorously, trying to make it up to the hole. The Doctor grabbing onto her mane with his mouth, his legs tightening around her stomach as he tried to stay on. At last Derpy reached the edge, grabbing it with her hooves, and using them and her frantically flapping wings to scramble out.

It felt good to be above the ground again, to feel the grass benieth her hooves and nothing but purple sky and bright blue plains as for as the eye could see.

"We made it, Doctor!" Derpy gasped triumphantly.

No answer. The weight on her back suddenly became heavier, and completely limp.

"Doctor?"

She turned her head and saw he was unconscious once more. He was still shivering and sweating, but his breathing seemed steadiler than when Derpy had first found him.

"Perhaps it's for the best," she whispered to herself, kissing the top of his head gently. It seemed like the only part of him that wasn't bruised or bleeding. "You're not in any pain right now."

Then she began to gallop once more, the long grass parting before her, and brushing against her coat. Above her the sky began to darken, to deepen. Twilight fell over the land, and stars beginning to shine far above the horizon.

Neither Derpy nor the Doctor saw the shadowy form of Taldusk as he stood, hidden in the tall grass. As he stood, watching the gray mare with the injured Time Lord on her back run, run to freedom.

"Run, Doctor," he whispered, a faint smile on his lips. "Run." *****

* * *

The Doctor was dreaming.

He was a young colt again, galloping through the scarlet grass under the light of the twin suns shinning in the burnt orange sky. He was laughing and playing with his friend Koschei, not a care in the world.

"Do the thing with your horn again," Koschei, urged.

So he did, bracing his legs against the ground, scrunching his eyes shut in concentration. For a moment, a faint green glow appeared at the tip of horn. Then it faded. He opened his eyes to see Koschei grinning at him and he grinned back.

"That... is _so _cool," Koschei breathed. "I wish I could do magic."

"Yeah, 's cool, but it's really hard. You'd never have the patience for it." The young colt snorted with laughter and cuffed his friend playfully. A second later they were tussing on the ground, the sound of their laughter ringing out across the field.

_Do you ever think about the lives you have stolen?_

The Doctor gasped, the air flooding out of his lungs, and suddenly he was himself again. The bright scenery plummeted into darkness, total blackness. But that was only the beginning. Voices, the voices of the dead were swirling all around him, taunting him, calling out from the darkness. Their words overlapped and tangled together, but there was one sentence that was all too clear.

_You killed us._

"I-I offered you a chance to go!" he cried out desperately, taking a step back. "You gave me no choice. I didn't want to kill you."

_You killed me. _

The voice was harsh and grating, but there was no mistaking it.

"N-n-no," the Doctor stammered, his voice almost a whimper. He slowly turned to face the voice, shaking his head again and again. "P-please, n-no. Not you. Not you, Koschei."

The shadows parted to reveal a blue-coated figure standing before him, grinning wickedly, his yellow eyes dark and insane. The Master.

The Master dropped the grin, then cocked his head to the side and asked, aslmost innocently, "Doctor... do you hear the drums?"

"_AHHHHHHHH!_" The Doctor dropped to his knees and screamed. He heard the drums, the everlasting drums, the drums that had driven the Master to insanity.

_Bum bum ba-bum. Bum bum ba-bum._

"On and on and on," the Master sang. "Never ending. Neeeeeever ending. The only escape is _death._"

He began to laugh and laugh, the laughter echoing through the darkness. It was almost as horrible as the drums, the never-ending drums.

The Doctor slapped his hooves over his ears and screamed again, trying, _trying _to block out the awful noise. But they echoed inside him, the drums, the never-ending drums.

* * *

"_Doctor!_"

The Doctor's eyes snapped open, his breathing coming in quick, short, gasps. His hearts were racing. He jerked his head up and saw Derpy staring at him, her eyes wide. He was back in the TARDIS, in a white room, lying on something soft. A blanket.

"I had just finished wrapping up your leg when you started twitching and saying 'No'," she said, her voice shaking slightly. "I tried to wake you up, but then you started thrashing around and screaming." She looked down. "Y-you kind of scared me."

"I had a nightmare," he whispered slowly, carefully moving into a sitting position. He took a shuddering breath as the dream flashed through his mind. _Calm. Keep it together._

But he could not. The walls of the dam could not hold the strain any longer, and they burst. The Doctor began to sob uncontrollably, tears flooding out of his eyes, his chest hitching.

"I didn't want to kill them," he choked out. "You have to believe me, I _didn't want to. _I'm sorry. I'm _so, so sorry._"

"Oh Doctor..."

He felt Derpy's arms wrap around his body, holding him close to her as he trembled. "I know," she whispered in his ear. "I... I know."

After a minute or so, the Doctor quieted, trying to pick up the scattered parts and piece himself back together. He pulled away from Derpy and wiped a hoof across his eyes, sniffing. "I'm sorry you had to see me like that," he sighed.

Derpy was quiet for a second, her eyes soft, then said. "Everyone has nightmares. Everyone loses it sometimes. Even you, Doctor."

The Doctor smiled sadly. "Yep, I'm afraid that's true." He looked down for a moment, then moved closer to Derpy. He lifted his hoof and gently smoothed her mussed hair. "Derpy, have I ever told you how lucky I am to have have you as my companion?"

Derpy blushed and looked down. "I just... I just want to be there for you when you need me. To go on adventures with you, help you up when you fall down."

"And that's why I'm so lucky to have you, sweet Bright Eyes," the Doctor told her with another smile.

* * *

**A/N:**

***If you're confused on why Taldusk didn't go after him, it's because his job is done. The Shadow Ponies never said they were going to kill him. It's not their job to stop "crimminals", only to serve them justice. It's often said when someone loses a friend or family memeber or whatever, it feels like a part of them is left behind. So, they literally took a part of the Doctor and left it behind. The broken leg and cuts and bruises were just thrown in for good measure.**


	3. Epilouge

"Derpy! Derpy I _did it!_"

"What is it, Doctor? What did you do? Can I see?"

"Ah, here it is!"

*buzz*

"Um... I don't get it."

"It's called a sonic screwdriver! I made it myself!"

"I still don't get it. It doesn't really look like a screwdriver, and it doesn't seem very... _sonic_."

"Oh Derpy, Derpy, _Derpy_. I-"

"What?"

"Ah _hem_. Well, I-"

"You got something in your throat, Doctor?"

"Der_py!_"

"Y_eeesss_?"

"You know what? Just-just... _phhbbbbttttt_."

"Sooo..."

"Hm?"

"What does it do, Doctor?"

"Well... to put it simply, it... _sonics_."

"Huh?"

"I'm not _exactly_ sure what all it can do, but hopefully, I've succeeded in  
getting some of the magic from what was left of my horn into it."

"O_hhh_, so it's full of-"

"Wibbly-woobly, timey-wimby, magic-y... _stuff_."

* * *

**A/N: Well, that's all folks! I just threw this in as a bonus, explaining where the Doctor got his sonic screwdriver. (Basically, up until now,his horn served as his sonic screwdriver) **

**Leave me a review with what you thought! **

**Oh, and BTW, I've got an illustration for this story posted on my Deviantart page. My username is Startoucher. I'm planning on posting more if you wanna check it out!**


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